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This paper presents the multiprocessor architecture of the Simultaneous Optical Multiprocessor Exchange Bus (SOME-Bus), and examines the performance of representative algorithms for matrix operations, merging and sorting, using the message-passing and distributed-shared-memory paradigms.
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The two soft-clipped BAM files were merged and sorted.
During clustering, K-tuples (contiguous DNA sequences that are K bases long) were merged and sorted into a table, and shared K-mer words were linked in a relation matrix.
Events from these traces are then merged and sorted by chronological order for processing.
K-tuples were merged and sorted into a table, and shared kmer words were linked in a relation matrix.
The rtracklayer package, however, will unfortunately merge and sort the query regions before coverage vectors are retrieved.
It further allows for the implementation of SAMtools to extract alignments in a region, merge and sort alignments and to complete SNP calls [ 20, 21].
Alignments were converted to the SAM format, then merged and sorted into one master binary alignment file (BAM format) with SAMtools 0.1.18.
Expression data and pathway information data for co-expressed genes (r > 0.5 for a maximum of 50 genes) were merged and sorted according to r-value.
K-tuples were then merged and sorted into a table so that kmer words shared by different reads could be linked.
We merged and sorted the alignment BED files for the three biological replicates under saline conditions and used BEDTools [ 45] to create a large BAM file that contains nearly 250 million alignments.
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